Non-B DNA Analysis Pipeline

Snakemake workflow that intersects human transcript annotations (GTF) with Non-B DNA structural-motif BED files and produces per-transcript feature summaries, enrichment tests, and statistical analyses comparing protein-coding and lncRNA transcripts.

Requirements

• Conda / Mamba (environments: workflow/envs/gfa.yaml, g4discovery.yaml)
• Snakemake ≥ 7
• Pre-computed Non-B DNA BED files in resources/GRCh38_NonBDNA/

Quick start

# copy and edit the default config
cp config/config.yaml config/config_mine.yaml

snakemake --snakefile Snakefile_integrated \
          --configfile config/config_mine.yaml \
          --use-conda -j 8

# Extended analysis only
snakemake --snakefile Snakefile_integrated \
          --configfile config/config_mine.yaml \
          --use-conda -j 8 extended_analysis_all

Analysis layers

Layer	Entry rule	Description
Basic	all	Per-motif overlap summaries + KDE distribution plots
Extended	extended_analysis_all	100+ feature extraction, chi-square contingency tests, univariate statistical tests, and Random Forest feature importance

Pipeline steps

Step	Rule	Output
1	create_transcripts_bed	transcripts.bed (BED6 from GTF)
1	create_biotypes_from_fasta	biotypes.tsv
1	prepare_transcript_ids	annotation/pc_transcript_ids.txt, lncrna_transcript_ids.txt
2	basic_motif_analysis	transcript_gfa.{motif}_summary.tsv, gfa.{motif}_distributions.png (×8 motifs)
3.1	extended_feature_extraction	extended_analysis/features_nonb_features.csv, features_nonb_summary.txt
3.2	extended_contingency_analysis	extended_analysis/contingency_motif_type_chi_square.csv, contingency_contingency_report.txt
3.3	extended_statistical_analysis	extended_analysis/statistics_univariate_tests.csv, statistics_feature_importance.csv
4	create_summary_report	complete_analysis_report.txt

All outputs are namespaced under results/{dataset}/.

Configs

File	Purpose
config/config.yaml	Default config (toy + gencode.v47 datasets)

Dev info

See nbd_pipeline_manifest.yaml for the full rule catalogue, known bugs, and script inventory.